Figure 2 — Crohn’s Disease SNP-Propagated Signalling Analysis

Description:
Figure 2 illustrates how Crohn’s disease (CD)-associated non-coding SNPs perturb key cellular processes including cytokine signalling, immune regulation, DNA repair, and apoptosis.

Panel A — SNP-Propagated Signalling Network
	•Software: Cytoscape
	•Cytoscape session: no_degree_CD_ppi_10k.cys
	•Notes: Proteins (nodes) grouped via Girvan–Newman modularisation; 
	major modules annotated using Reactome enrichment. The enriched pathways 
	are in Dataset EV2. Coloured edges highlight module associations. Node 
	size indicates patient frequency.

Panel B — Protein Frequency Distribution
	•Input file: cd_only_ppi10rnd.txt
    •Code file: Figure2_b.rmd R notebook
	•Description: Frequency distribution of SNP-propagated proteins across CD patients.

Panel C — Reactome Pathway Enrichment
	•Input files:
		•cd_only_ppi10rnd.txt
		•ReactomePathways.gmt (Reactome gene set library)
		•OmniPath_27_10_2021_directed.ncol
	•Output file: Reactome_CD_PPI_100_cutoff_ora_results.csv
	•Description: Over-representation analysis (ORA) of Reactome pathways for proteins perturbed in ≥100 patients.